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fix: solve issues with variant_export_external and re-enable wgs_cnv_export_external #354

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Nicolai-vKuegelgen
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@Nicolai-vKuegelgen Nicolai-vKuegelgen commented Jan 17, 2023

re-enable wgs_cnv_export_external:

  • the 'wgs_cnv_export_external' was removed from the snappy_snake app by accident. I has now been re-added

solve issues with variant_export_external:

  • changes in the wrapper for varfish_annotator broke the 'variant_export_external' step, since it also relies on this. The expected log files and output links/files have been updated.

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  • Please format your Python code with black: make black
  • Please format your Snakemake code with snakefmt: make snakefmt
  • Please organize your imports isorts: make isort
  • Please ensure that your code passes flake8: make flake8

You can trigger all lints locally by running make lint

@Nicolai-vKuegelgen Nicolai-vKuegelgen changed the title Fix: add wgs_cnv_expoert_external back fix: add wgs_cnv_expoert_external back Jan 17, 2023
@Nicolai-vKuegelgen Nicolai-vKuegelgen changed the title fix: add wgs_cnv_expoert_external back fix: solve issues with variant_export_external and re-enable wgs_cnv_export_external Jan 17, 2023
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Coverage Status

Coverage: 83.422% (-1.2%) from 84.613% when pulling 20a590e on 353-wgs_cnv_export_external-step-was-removed-from-snappy-snale into 5ecad1a on main.

@Nicolai-vKuegelgen
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@holtgrewe I'm not sure what I'd need to do to solve the coverage issue (or if it's even necessary given that this fixes a critical issue).

@holtgrewe holtgrewe merged commit 47d9e33 into main Jan 17, 2023
@holtgrewe holtgrewe deleted the 353-wgs_cnv_export_external-step-was-removed-from-snappy-snale branch January 17, 2023 13:59
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@Nicolai-vKuegelgen ;-)

@tedil tedil mentioned this pull request Jun 28, 2024
This was referenced Dec 9, 2024
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wgs_cnv_export_external step was removed from snappy snale
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